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- PDB-5v53: Crystal structure of the D141A/Q233E/N240D variant of catalase-pe... -

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Basic information

Entry
Database: PDB / ID: 5v53
TitleCrystal structure of the D141A/Q233E/N240D variant of catalase-peroxidase from B. pseudomallei with acetate bound
ComponentsCatalase-peroxidase
KeywordsOXIDOREDUCTASE / catalase / peroxidase / D141A/Q233E/N240D / heme / acetate
Function / homology
Function and homology information


catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding
Similarity search - Function
Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase ...Catalase-peroxidase haem / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Peroxidase; domain 1 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / PHOSPHATE ION / Catalase-peroxidase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLoewen, P.C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)D9600 Canada
CitationJournal: Biochemistry / Year: 2017
Title: The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine.
Authors: Machuqueiro, M. / Victor, B. / Switala, J. / Villanueva, J. / Rovira, C. / Fita, I. / Loewen, P.C.
History
DepositionMar 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catalase-peroxidase
B: Catalase-peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,18418
Polymers158,9902
Non-polymers2,19516
Water26,3921465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12290 Å2
ΔGint-165 kcal/mol
Surface area50490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.842, 115.825, 174.775
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 36 - 748 / Label seq-ID: 16 - 728

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Catalase-peroxidase / / CP / Peroxidase/catalase


Mass: 79494.945 Da / Num. of mol.: 2 / Mutation: D141A, Q233E, N240D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria)
Strain: 1710b / Gene: katG, BURPS1710b_3366 / Plasmid: pKS / Production host: Escherichia coli (E. coli) / Strain (production host): UM262 / References: UniProt: Q3JNW6, catalase-peroxidase

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Non-polymers , 8 types, 1481 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1465 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.45 % / Mosaicity: 0.17 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 9, 2015 / Details: mirrors
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→46.23 Å / Num. all: 214623 / Num. obs: 214623 / % possible obs: 96.1 % / Redundancy: 3.9 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.07 / Rsym value: 0.061 / Net I/av σ(I): 8.6 / Net I/σ(I): 11.7 / Num. measured all: 827169
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRpim(I) allRrim(I) allRsym value% possible all
1.7-1.793.80.5381.4320210.310.6240.53898.7
1.79-1.93.80.342.30.1950.3940.3498.3
1.9-2.033.80.2083.70.1190.2410.20897.9
2.03-2.193.80.1335.70.0760.1540.13397
2.19-2.43.90.0928.10.0520.1060.09296.2
2.4-2.693.90.06910.30.0390.080.06995.4
2.69-3.13.90.05512.10.0310.0630.05594.1
3.1-3.83.90.04314.60.0240.050.04392.2
3.8-5.3840.03717.20.020.0420.03791.2
5.38-46.233.90.03219.80.0180.0360.03287.9

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MWV

1mwv
PDB Unreleased entry


Resolution: 1.7→46.23 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.09 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0718 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.075 / Details: MOLECULAR REPLACEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1722 10697 5 %RANDOM
Rwork0.1419 ---
obs0.1434 203772 95.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.9 Å2 / Biso mean: 25.554 Å2 / Biso min: 11.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2--1.41 Å20 Å2
3----0.64 Å2
Refinement stepCycle: final / Resolution: 1.7→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11004 0 144 1465 12613
Biso mean--32.89 33.91 -
Num. residues----1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.01911544
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210438
X-RAY DIFFRACTIONr_angle_refined_deg2.4541.94915722
X-RAY DIFFRACTIONr_angle_other_deg1.246324099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96451448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58323.591543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.135151755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9951590
X-RAY DIFFRACTIONr_chiral_restr0.1810.21655
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02113186
X-RAY DIFFRACTIONr_gen_planes_other0.0120.022534
Refine LS restraints NCS

Ens-ID: 1 / Number: 47218 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 816 -
Rwork0.217 15386 -
all-16202 -
obs--98.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0221-0.0224-0.02260.10980.08880.15550.00980.0057-0.0157-0.0001-0.0056-0.00840.02330.0117-0.00420.01680.0041-0.00620.0093-0.00830.0216-24.4275-62.2534-20.9039
20.1066-0.0020.02810.0312-0.01420.0871-0.0174-0.0140.0033-0.00540.0172-0.0138-0.00870.01430.00020.0141-0.0072-0.00540.0214-0.00670.0134-9.5315-33.39525.6323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 809
2X-RAY DIFFRACTION2B36 - 807

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